search

openforcefield / cmiles

Generate canonical molecule identifiers for quantum chemistry database
https://cmiles.readthedocs.io
MIT License
23 stars 7 forks source link

Canonical atom order without resorting to omega #11

Closed ChayaSt closed 5 years ago

ChayaSt commented 5 years ago

We want to have a canonical order for the map indices in the mapped SMILES. Currently, cmiles uses the setting omega.SetCanonOrder(True) and generates a conformer which has a canonical atom order that is used to generate the map. However, I want to avoid having to use omega since it can be slow for larger molecules.

oechem has a function OECanonicalOrderAtoms that is supposed to reorder the atoms, but it doesn't change the indices and the new order is not the same canonical order as the one in omega. @j-wags, do you have any insight on this?

j-wags commented 5 years ago

Unfortunately, I don't have much experience dealing with canonicalization. Though, I'll follow this issue because I'd like to know what OE/RDK will/can do in terms of reordering atom indices.

ChayaSt commented 5 years ago

Addressed by #13